spike branch updated from latest features/JAL-2446

[jalview.git] / src / jalview / appletgui / AnnotationLabels.java

diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index 487d130..3f7e523 100755 (executable)
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -339,7 +339,8 @@ public class AnnotationLabels extends Panel implements ActionListener,
                 av.calcPanelHeight());
         f.height += dif;
         ap.seqPanelHolder.setPreferredSize(f);
-        ap.setScrollValues(av.getStartRes(), av.getStartSeq());
+        ap.setScrollValues(av.getRanges().getStartRes(), av.getRanges()
+                .getStartSeq());
         ap.validate();
         // ap.paintAlignment(true);
         ap.addNotify();
@@ -712,11 +713,47 @@ public class AnnotationLabels extends Panel implements ActionListener,
             // todo: make the ap scroll to the selection - not necessary, first
             // click highlights/scrolls, second selects
             ap.seqPanel.ap.idPanel.highlightSearchResults(null);
-            ap.av.setSelectionGroup(// new SequenceGroup(
-            aa[selectedRow].groupRef); // );
-            ap.av.sendSelection();
+            // process modifiers
+            SequenceGroup sg = ap.av.getSelectionGroup();
+            if (sg == null
+                    || sg == aa[selectedRow].groupRef
+                    || !(jalview.util.Platform.isControlDown(evt) || evt
+                            .isShiftDown()))
+            {
+              if (jalview.util.Platform.isControlDown(evt)
+                      || evt.isShiftDown())
+              {
+                // clone a new selection group from the associated group
+                ap.av.setSelectionGroup(new SequenceGroup(
+                        aa[selectedRow].groupRef));
+              }
+              else
+              {
+                // set selection to the associated group so it can be edited
+                ap.av.setSelectionGroup(aa[selectedRow].groupRef);
+              }
+            }
+            else
+            {
+              // modify current selection with associated group
+              int remainToAdd = aa[selectedRow].groupRef.getSize();
+              for (SequenceI sgs : aa[selectedRow].groupRef.getSequences())
+              {
+                if (jalview.util.Platform.isControlDown(evt))
+                {
+                  sg.addOrRemove(sgs, --remainToAdd == 0);
+                }
+                else
+                {
+                  // notionally, we should also add intermediate sequences from
+                  // last added sequence ?
+                  sg.addSequence(sgs, --remainToAdd == 0);
+                }
+              }
+            }
             ap.paintAlignment(false);
             PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
+            ap.av.sendSelection();
           }
           else
           {
@@ -801,12 +838,9 @@ public class AnnotationLabels extends Panel implements ActionListener,
             + sq.getSequenceAsString() + "\n");
     if (av.hasHiddenColumns())
     {
-      jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector();
-      for (int[] region : av.getColumnSelection().getHiddenColumns())
-      {
-        jalview.appletgui.AlignFrame.copiedHiddenColumns
-                .addElement(new int[] { region[0], region[1] });
-      }
+      jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector<>(
+              av.getAlignment().getHiddenColumns()
+                      .getHiddenColumnsCopy());
     }
   }